You're right about the long-term plan, unfortunately you can't say they are either completely alive or completely dead, since they are in the process of thawing :( You certainly can't say they're dead.
We can't do a "door shut" approach in Bazel, we need to migrate things one problem at a time. The incompatibility I'm in the process of introducing is a requirement that what used to be top-level symbols in Bazel (like JavaInfo, cc_common) can only be used through their rightful repositories. This will need a migration of a "relatively small" set of repositories that are breaking these rules.
Another evidence the repositories are still required are buildifier warnings to load rules from these repositories.
I don't want to tell the users with the next LTS or one after - "sorry all top-level symbols and rules are gone - please migrate to use the new release".
The decision if you want to use rules_java and rules_cc is still yours. If you only need rules (not modules or providers) and want to ignore buildifier warnings, feel free to use them directly. The warning is that the migration is going to get harder with time.
About lagging - we need to fix those. And we need to stop putting everything into bazel_tools, just because it's cosy.